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Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis

2006; Cell Press; Volume: 126; Issue: 6 Linguagem: Inglês

10.1016/j.cell.2006.08.003

1097-4172

Xiaoyu Zhang, Junshi Yazaki, Ambika Sundaresan, Shawn Cokus, Wan Chan, Huaming Chen, Ian R. Henderson, Paul Shinn, Matteo Pellegrini, Steve Jacobsen, Joseph R. Ecker,

Plant nutrient uptake and metabolism

Cytosine methylation is important for transposon silencing and epigenetic regulation of endogenous genes, although the extent to which this DNA modification functions to regulate the genome is still unknown. Here we report the first comprehensive DNA methylation map of an entire genome, at 35 base pair resolution, using the flowering plant Arabidopsis thaliana as a model. We find that pericentromeric heterochromatin, repetitive sequences, and regions producing small interfering RNAs are heavily methylated. Unexpectedly, over one-third of expressed genes contain methylation within transcribed regions, whereas only ∼5% of genes show methylation within promoter regions. Interestingly, genes methylated in transcribed regions are highly expressed and constitutively active, whereas promoter-methylated genes show a greater degree of tissue-specific expression. Whole-genome tiling-array transcriptional profiling of DNA methyltransferase null mutants identified hundreds of genes and intergenic noncoding RNAs with altered expression levels, many of which may be epigenetically controlled by DNA methylation.